Variant report

Variant	rs6873523
Chromosome Location	chr5:177572927-177572928
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:88)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:88 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr5:177572561-177579123	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr5:177572900-177573353	A549	lung:	n/a	n/a
3	RAD21	chr5:177572866-177573431	A549	lung:	n/a	n/a
4	BCL3	chr5:177572873-177573803	A549	lung:	n/a	n/a
5	RAD21	chr5:177572713-177573963	MCF-7	breast:	n/a	n/a
6	CTCF	chr5:177572739-177573825	HCT-116	colon:	n/a	n/a
7	MTA3	chr5:177572789-177573656	GM12878	blood:	n/a	n/a
8	MAX	chr5:177572629-177575909	MCF-7	breast:	n/a	n/a
9	RUNX3	chr5:177572909-177573546	GM12878	blood:	n/a	n/a
10	CTCF	chr5:177572871-177573373	A549	lung:	n/a	n/a
11	CHD2	chr5:177572892-177573319	K562	blood:	n/a	n/a
12	POLR2A	chr5:177572810-177575049	K562	blood:	n/a	n/a
13	POLR2A	chr5:177563930-177577112	K562	blood:	n/a	n/a
14	POLR2A	chr5:177572576-177573984	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr5:177572797-177576470	GM12878	blood:	n/a	n/a
16	RAD21	chr5:177572721-177573896	MCF-7	breast:	n/a	n/a
17	ZEB1	chr5:177572904-177573495	GM12878	blood:	n/a	n/a
18	SMC3	chr5:177572793-177573734	Hela-S3	cervix:	n/a	n/a
19	POLR2A	chr5:177572694-177575959	GM12892	blood:	n/a	n/a
20	POLR2A	chr5:177572902-177573454	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr5:177572627-177574210	H1-hESC	embryonic stem cell:	n/a	n/a
22	POLR2A	chr5:177572927-177573387	GM12878	blood:	n/a	n/a
23	POLR2A	chr5:177572629-177581352	GM12891	blood:	n/a	n/a
24	POLR2A	chr5:177572615-177580157	SK-N-MC	brain:	n/a	n/a
25	CEBPB	chr5:177572829-177574632	MCF-7	breast:	n/a	n/a
26	TFAP2A	chr5:177572567-177573870	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr5:177572877-177573320	HCT-116	colon:	n/a	n/a
28	CTCF	chr5:177572678-177573661	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr5:177572795-177574684	HepG2	liver:	n/a	n/a
30	POLR2A	chr5:177572914-177573385	H1-hESC	embryonic stem cell:	n/a	n/a
31	POLR2A	chr5:177572682-177577334	GM12878	blood:	n/a	n/a
32	MAX	chr5:177572813-177574050	MCF-7	breast:	n/a	n/a
33	NR2F2	chr5:177572643-177574714	MCF-7	breast:	n/a	n/a
34	PML	chr5:177572672-177573716	GM12878	blood:	n/a	n/a
35	POLR2A	chr5:177572865-177574552	GM12878	blood:	n/a	n/a
36	POLR2A	chr5:177572693-177579145	PFSK-1	brain:	n/a	n/a
37	POLR2A	chr5:177572844-177573343	HCT-116	colon:	n/a	n/a
38	POLR2A	chr5:177572838-177573447	K562	blood:	n/a	n/a
39	GATA3	chr5:177572848-177577152	MCF-7	breast:	n/a	chr5:177574913-177574921 chr5:177574691-177574701
40	GATA3	chr5:177572630-177574301	MCF-7	breast:	n/a	n/a
41	RAD21	chr5:177572798-177573462	H1-hESC	embryonic stem cell:	n/a	n/a
42	CTCF	chr5:177572822-177573524	HCT-116	colon:	n/a	n/a
43	CTCF	chr5:177572782-177573321	HepG2	liver:	n/a	n/a
44	TBL1XR1	chr5:177572771-177573341	K562	blood:	n/a	n/a
45	POLR2A	chr5:177572616-177581328	MCF10A-Er-Src	breast:	n/a	n/a
46	JUND	chr5:177572920-177573376	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr5:177572861-177576487	HepG2	liver:	n/a	n/a
48	CTCF	chr5:177572890-177573353	H1-hESC	embryonic stem cell:	n/a	n/a
49	POLR2A	chr5:177572636-177576075	HL-60	blood:	n/a	n/a
50	CTCF	chr5:177572626-177574010	MCF-7	breast:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:177556060..177559089-chr5:177572421..177574313,3	K562	blood:
2	chr1:149222391..149224886-chr5:177572662..177574353,2	MCF-7	breast:
3	chr5:177556060..177559207-chr5:177571980..177574313,5	K562	blood:
4	chr5:177572705..177577722-chr5:177630592..177633512,5	MCF-7	breast:

No data

Variant related genes	Relation type
RMND5B	TF binding region
ENSG00000206737	Chromatin interaction
ENSG00000197451	Chromatin interaction
ENSG00000145916	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10035478	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10042021	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10060446	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10074810	0.84[JPT][hapmap]
rs11948118	0.87[ASN][1000 genomes]
rs12655707	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13165989	0.81[ASN][1000 genomes]
rs13175750	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13185017	0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13189047	0.82[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13436876	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34093388	0.84[ASN][1000 genomes]
rs34353050	0.81[ASN][1000 genomes]
rs35027513	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35598853	0.80[ASN][1000 genomes]
rs35885458	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs36087128	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3812074	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3812075	0.82[CEU][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.83[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3812079	0.81[ASW][hapmap];0.83[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3812080	0.84[GIH][hapmap]
rs4549545	0.83[MEX][hapmap]
rs4637566	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6601217	0.81[ASW][hapmap];0.88[CEU][hapmap];0.84[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.84[JPT][hapmap];0.87[LWK][hapmap];0.81[MEX][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6601220	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6893797	0.88[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7379278	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[GIH][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7380934	1.00[GIH][hapmap];0.88[MEX][hapmap];0.82[TSI][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7380947	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7447860	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7448252	0.84[JPT][hapmap]
rs7701678	0.94[GIH][hapmap];0.88[MEX][hapmap]
rs7716860	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7732415	0.89[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.86[TSI][hapmap];0.82[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7733574	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1021198	chr5:177386267-177611648	Enhancers Bivalent/Poised TSS Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	nsv1029398	chr5:177502106-178070654	Flanking Active TSS Enhancers Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	136 gene(s)	inside rSNPs	diseases
4	nsv462567	chr5:177505021-177572927	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv471058	chr5:177505021-177572927	Enhancers Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
6	nsv600392	chr5:177505021-177572927	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv1019404	chr5:177507080-177859089	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	126 gene(s)	inside rSNPs	diseases
8	nsv883190	chr5:177532201-177620189	Flanking Active TSS Active TSS Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv600394	chr5:177549491-177608195	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv965520	chr5:177570961-177577311	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	esv3352132	chr5:177572746-177576144	Genic enhancers Strong transcription Weak transcription Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6873523	PARL	trans	cerebellum	SCAN
rs6873523	DCTN3	trans	parietal	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:177558800-177576800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr5:177559000-177574000	Weak transcription	Small Intestine	intestine
3	chr5:177559000-177580000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:177559000-177580000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:177559200-177573000	Weak transcription	Psoas Muscle	Psoas
6	chr5:177559200-177573200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr5:177559200-177579800	Weak transcription	Right Atrium	heart
8	chr5:177559800-177577600	Weak transcription	Fetal Brain Male	brain
9	chr5:177560200-177579400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr5:177560200-177579600	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr5:177560200-177579800	Strong transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:177560400-177578400	Strong transcription	Primary monocytes fromperipheralblood	blood
13	chr5:177560400-177578400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr5:177560400-177578600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr5:177560600-177579400	Strong transcription	Fetal Intestine Small	intestine
16	chr5:177560800-177579400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr5:177560800-177579600	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:177561000-177578000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr5:177561000-177578200	Strong transcription	Adipose Nuclei	Adipose
20	chr5:177561000-177578800	Strong transcription	Thymus	Thymus
21	chr5:177561000-177579200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:177561000-177579400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:177561000-177579800	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr5:177561200-177578800	Strong transcription	Primary T cells from cord blood	blood
25	chr5:177561200-177579400	Strong transcription	Fetal Thymus	thymus
26	chr5:177562200-177577400	Strong transcription	Primary neutrophils fromperipheralblood	blood
27	chr5:177562200-177578800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr5:177566800-177576400	Strong transcription	Dnd41	blood
29	chr5:177566800-177576800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr5:177567000-177578000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr5:177567000-177578200	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr5:177567000-177578800	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr5:177567000-177579000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr5:177567200-177578600	Strong transcription	Sigmoid Colon	Sigmoid Colon
35	chr5:177567400-177579000	Strong transcription	Fetal Brain Female	brain
36	chr5:177568000-177578600	Strong transcription	HepG2	liver
37	chr5:177568000-177578800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:177568200-177579400	Strong transcription	Duodenum Mucosa	Duodenum
39	chr5:177568400-177578600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:177568400-177578600	Strong transcription	Colonic Mucosa	Colon
41	chr5:177568600-177576200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr5:177568800-177576400	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr5:177568800-177576400	Strong transcription	Brain Hippocampus Middle	brain
44	chr5:177568800-177577000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr5:177568800-177577200	Strong transcription	Right Ventricle	heart
46	chr5:177568800-177578600	Strong transcription	Left Ventricle	heart
47	chr5:177568800-177578800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
48	chr5:177568800-177579600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr5:177569000-177578600	Strong transcription	Brain Germinal Matrix	brain
50	chr5:177569000-177579000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

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